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- PDB-9hxt: Crystal structure of bifunctional catalase-phenol oxidase from a ... -

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Basic information

Entry
Database: PDB / ID: 9hxt
TitleCrystal structure of bifunctional catalase-phenol oxidase from a marine-derived Cladosporium species
ComponentsCatalase-phenol oxidase from Cladosporium sp
KeywordsOXIDOREDUCTASE / catalase / phenol-oxidase / Cladosporium / bioremediation / marine-derived biocatalyst
Function / homology
Function and homology information


catalase activity / hydrogen peroxide catabolic process / response to hydrogen peroxide / peroxisome / heme binding / mitochondrion / metal ion binding
Similarity search - Function
Catalase, mono-functional, haem-containing, clades 1 and 3 / Catalase / Catalase immune-responsive domain / Catalase-related immune-responsive / Catalase active site / Catalase proximal active site signature. / Catalase core domain / Catalase, mono-functional, haem-containing / Catalase / catalase family profile. / Catalase superfamily
Similarity search - Domain/homology
ALANINE / GLYCINE / PROTOPORPHYRIN IX CONTAINING FE / 3,6,9,12,15-PENTAOXAHEPTADECANE / 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE / DI(HYDROXYETHYL)ETHER / SERINE / Catalase core domain-containing protein
Similarity search - Component
Biological speciesCladosporium sp. TM138-S3 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsKosinas, C. / Ferousi, C. / Pantelakis, O.I. / Topakas, E. / Dimarogona, M.
Funding support Greece, 1items
OrganizationGrant numberCountry
Hellenic Foundation for Research and Innovation (HFRI)15024 Greece
CitationJournal: To Be Published
Title: Crystal structure of bifunctional catalase-phenol oxidase from a marine-derived Cladosporium species
Authors: Kosinas, C. / Ferousi, C. / Topakas, E. / Dimarogona, M.
History
DepositionJan 8, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Catalase-phenol oxidase from Cladosporium sp
A: Catalase-phenol oxidase from Cladosporium sp
B: Catalase-phenol oxidase from Cladosporium sp
C: Catalase-phenol oxidase from Cladosporium sp
D: Catalase-phenol oxidase from Cladosporium sp
E: Catalase-phenol oxidase from Cladosporium sp
F: Catalase-phenol oxidase from Cladosporium sp
G: Catalase-phenol oxidase from Cladosporium sp
hetero molecules


Theoretical massNumber of molelcules
Total (without water)508,57349
Polymers497,8128
Non-polymers10,76141
Water92,2735122
1
H: Catalase-phenol oxidase from Cladosporium sp
E: Catalase-phenol oxidase from Cladosporium sp
F: Catalase-phenol oxidase from Cladosporium sp
G: Catalase-phenol oxidase from Cladosporium sp
hetero molecules


Theoretical massNumber of molelcules
Total (without water)253,32821
Polymers248,9064
Non-polymers4,42217
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Catalase-phenol oxidase from Cladosporium sp
B: Catalase-phenol oxidase from Cladosporium sp
C: Catalase-phenol oxidase from Cladosporium sp
D: Catalase-phenol oxidase from Cladosporium sp
hetero molecules


Theoretical massNumber of molelcules
Total (without water)255,24528
Polymers248,9064
Non-polymers6,33924
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.549, 92.663, 169.229
Angle α, β, γ (deg.)83.31, 78.177, 60.329
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 8 molecules HABCDEFG

#1: Protein
Catalase-phenol oxidase from Cladosporium sp


Mass: 62226.488 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cladosporium sp. TM138-S3 (fungus) / Gene: WHR41_05493 / Production host: Komagataella pastoris (fungus) / References: UniProt: A0AB34KRF0

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Sugars , 3 types, 11 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1235.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3[DManpa1-3DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1_f3-g1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#12: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 10 types, 5152 molecules

#4: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Chemical ChemComp-SER / SERINE


Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO3
#9: Chemical ChemComp-ALA / ALANINE


Type: L-peptide linking / Mass: 89.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2
#10: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H5NO2
#11: Chemical ChemComp-P4G / 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE


Mass: 162.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C8H18O3
#13: Chemical ChemComp-P3G / 3,6,9,12,15-PENTAOXAHEPTADECANE


Mass: 250.332 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O5
#14: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5122 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 50.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 10% w/v PEG 20000, 20% v/v PEG MME 550, 0.02 M of each amino acid, 0.1 M MES/imidazole pH 6.5 Aminoacids: sodium L-glutamate, 0.2 M DL-alanine, 0.2 M glycine, 0.2 M DL-lysine HCl, 0.2 M DL-serine.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 8, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.6→82.944 Å / Num. obs: 577755 / % possible obs: 91.3 % / Redundancy: 3 % / CC1/2: 0.995 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.061 / Rrim(I) all: 0.086 / Net I/σ(I): 7
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.729 / Num. unique obs: 26249 / CC1/2: 0.549 / Rpim(I) all: 0.729 / Rrim(I) all: 1.032

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
REFMAC5.8.0425refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→82.944 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.913 / SU B: 4.77 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.105 / ESU R Free: 0.106
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2364 29038 5.032 %RANDOM
Rwork0.1994 547998 --
all0.201 ---
obs-577036 91.452 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 20.197 Å2
Baniso -1Baniso -2Baniso -3
1--0.872 Å20.206 Å20.507 Å2
2--0.702 Å20.097 Å2
3---0.123 Å2
Refinement stepCycle: LAST / Resolution: 1.6→82.944 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms32589 0 725 5122 38436
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01234745
X-RAY DIFFRACTIONr_bond_other_d0.0010.01631064
X-RAY DIFFRACTIONr_angle_refined_deg1.9391.84147329
X-RAY DIFFRACTIONr_angle_other_deg0.7061.78771340
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.18654146
X-RAY DIFFRACTIONr_dihedral_angle_2_deg13.0865260
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.72105417
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.322101862
X-RAY DIFFRACTIONr_chiral_restr0.110.24842
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0242680
X-RAY DIFFRACTIONr_gen_planes_other0.0030.028878
X-RAY DIFFRACTIONr_nbd_refined0.230.27559
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2010.231000
X-RAY DIFFRACTIONr_nbtor_refined0.1860.216784
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.217491
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.23052
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1270.217
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3160.236
X-RAY DIFFRACTIONr_nbd_other0.2550.2115
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2110.241
X-RAY DIFFRACTIONr_mcbond_it1.0471.21916422
X-RAY DIFFRACTIONr_mcbond_other1.0471.21916422
X-RAY DIFFRACTIONr_mcangle_it1.4462.1920595
X-RAY DIFFRACTIONr_mcangle_other1.4462.1920596
X-RAY DIFFRACTIONr_scbond_it1.6491.38118323
X-RAY DIFFRACTIONr_scbond_other1.6491.38118324
X-RAY DIFFRACTIONr_scangle_it2.4232.46326725
X-RAY DIFFRACTIONr_scangle_other2.4232.46326726
X-RAY DIFFRACTIONr_lrange_it3.52813.35641382
X-RAY DIFFRACTIONr_lrange_other3.52813.35741383
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.6-1.6420.27918670.248366190.249466210.9460.95782.55080.25
1.642-1.6870.25620820.222402230.224455950.9560.96692.78430.223
1.687-1.7350.24420320.208391410.21441390.9580.9793.28030.206
1.735-1.7890.23119470.187382840.189430740.9640.97793.39970.183
1.789-1.8470.2220190.178367660.18416210.9680.97993.18610.172
1.847-1.9120.23919670.191353410.194402580.9620.97692.67230.183
1.912-1.9840.25118220.213338870.215389270.9510.96391.73320.2
1.984-2.0650.23117030.182326380.184374470.9590.97791.70560.172
2.065-2.1570.22717840.183303720.186358330.9610.97489.73850.172
2.157-2.2620.23814410.19272390.193343100.9560.97183.59080.179
2.262-2.3850.23115060.175282330.178326040.9640.97991.21270.169
2.385-2.5290.21914460.176279080.178307730.9650.97895.38880.171
2.529-2.7040.22713800.18260810.183289670.9640.97694.8010.177
2.704-2.920.23712310.191243260.193270090.9570.97394.6240.19
2.92-3.1980.2411400.201222080.203248580.9570.9793.92550.202
3.198-3.5750.23911070.206195680.207224250.9580.9792.19620.207
3.575-4.1270.2178720.203163640.203197310.9640.96987.35490.206
4.127-5.0510.2287250.206141830.207167230.9590.96689.14670.211
5.051-7.130.266540.237120230.238129400.9520.9697.96750.246
7.13-82.9440.2853130.25265950.25371190.9440.95597.03610.279
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.3840.04460.00870.2752-0.03840.45210.00820.05190.0716-0.025-0.0012-0.0218-0.05030.072-0.0070.0502-0.0137-0.00960.03220.00260.0286-16.696170.932154.1386
20.3521-0.16350.03850.446-0.08310.3032-0.0017-0.05240.00690.05230.0065-0.04560.00850.0466-0.00480.0166-0.0005-0.00710.0173-0.00120.0056-1.67642.7405-2.3578
30.3756-0.15580.02460.3465-0.05370.27120.01730.03770.0972-0.0302-0.0067-0.0039-0.0956-0.024-0.01060.05050.00650.0050.01030.00940.0344-22.224134.7946-27.5907
40.4594-0.0749-0.12240.27770.03640.35090.0007-0.0086-0.0440.0248-0.00550.0860.0263-0.07790.00480.0247-0.0079-0.00670.02040.00230.0365-35.38954.6516-7.7184
50.4407-0.0878-0.13140.33660.04220.3610.01690.08380.0061-0.0827-0.0083-0.0268-0.0090.0235-0.00860.04850.0057-0.00740.0241-0.00260.0092-3.59138.963-40.2527
60.32410.02520.06110.2348-0.0090.64560.03050.0595-0.0608-0.035-0.0043-0.00050.11220.0221-0.02620.08360.0032-0.0220.012-0.01010.0345-35.750839.910541.8812
70.25850.00720.07630.22550.09390.55280.0059-0.0478-0.03840.06310.0154-0.03390.08080.058-0.02140.06280.0123-0.02030.03850.00430.029-17.772351.73981.924
80.37530.0462-0.07650.2602-0.00440.36340.007-0.0521-0.00960.0565-0.00350.06840.0322-0.0815-0.00340.0658-0.0199-0.01150.04680.0090.0328-53.937449.540468.8809
Refinement TLS groupSelection: ALL

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